Format with latest version of styler (#341)

R/aaa-utilities.R

@@ -161,11 +161,10 @@
     "ggplot2::geom_linerange(",
     "data = mapData,",
     "mapping = aes_string(",
-    switch(
-      direction,
+    switch(direction,
       "vertical" = "x = mapLabels$x, ymin = mapLabels$ymin, ymax = mapLabels$y,",
       "horizontal" = "y = mapLabels$y, xmin = mapLabels$xmin, xmax = mapLabels$x,"
-      ),
+    ),
     "color = mapLabels$color",
     "),",
     'size = .getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$size, position = 0, aesthetic = "size"),',
@@ -177,11 +176,10 @@
     "ggplot2::geom_linerange(",
     "data = mapData,",
     "mapping = aes_string(",
-    switch(
-      direction,
+    switch(direction,
       "vertical" = "x = mapLabels$x, ymin = mapLabels$y, ymax = mapLabels$ymax,",
       "horizontal" = "y = mapLabels$y, xmin = mapLabels$x, xmax = mapLabels$xmax,"
-      ),
+    ),
     "color = mapLabels$color",
     "),",
     'size = .getAestheticValues(n = 1, selectionKey = plotConfiguration$errorbars$size, position = 0, aesthetic = "size"),',

R/boxwhisker-get-measure.R

@@ -19,7 +19,6 @@ getBoxWhiskerMeasure <- function(data,
                                  y = NULL,
                                  group = NULL,
                                  quantiles = c(0.05, 0.25, 0.5, 0.75, 0.95)) {
-
   # If no data mapping is input, use default
   variableNames <- names(data)
   y <- y %||% utils::tail(variableNames, 1)

R/datamapping-range.R

@@ -35,7 +35,6 @@ RangeDataMapping <- R6::R6Class(
                           size = NULL,
                           group = NULL,
                           data = NULL) {
-
       # .smartMapping is available in utilities-mapping.R
       smartMap <- .smartMapping(data)
       super$initialize(x %||% smartMap$x,

R/datamapping-xygroup.R

@@ -31,7 +31,6 @@ XYGDataMapping <- R6::R6Class(
                           size = NULL,
                           group = NULL,
                           data = NULL) {
-
       # .smartMapping is available in utilities-mapping.R
       smartMap <- .smartMapping(data)
       super$initialize(x = x %||% smartMap$x, y = y %||% smartMap$y)

R/obs-vs-pred-datamapping.R

@@ -25,7 +25,7 @@ ObsVsPredDataMapping <- R6::R6Class(
     #' To map a loess smoother to the plot, use `smoother`="loess"
     #' @param ... parameters inherited from `XYGDataMapping`
     #' @return A new `ObsVsPredDataMapping` object
-    initialize = function(x = NULL, 
+    initialize = function(x = NULL,
                           y = NULL,
                           xmin = NULL,
                           xmax = NULL,
@@ -35,14 +35,14 @@ ObsVsPredDataMapping <- R6::R6Class(
       validateIsIncluded(smoother, c("lm", "loess"), nullAllowed = TRUE)
       validateIsString(xmin, nullAllowed = TRUE)
       validateIsString(xmax, nullAllowed = TRUE)
-      super$initialize(x=x,y=y,...)
+      super$initialize(x = x, y = y, ...)
       self$lines <- lines
       self$smoother <- smoother
       # If no xmin/xmax defined, map to x to get emtpy errorbars
       self$xmin <- xmin %||% self$x
       self$xmax <- xmax %||% self$x
     },
-    
+
     #' @description Check that `data` variables include map variables
     #' @param data data.frame to check
     #' @param metaData list containing information on `data`

R/pkratio-datamapping.R

@@ -12,7 +12,7 @@ PKRatioDataMapping <- R6::R6Class(
     ymin = NULL,
     #' @field ymax mapping of lower value of error bars around scatter points
     ymax = NULL,
-    
+
     #' @description Create a new `PKRatioDataMapping` object
     #' @param x Name of x variable to map
     #' @param y Name of y variable to map
@@ -21,15 +21,15 @@ PKRatioDataMapping <- R6::R6Class(
     #' @param lines List of ratio limits to display as horizontal lines
     #' @param ... parameters inherited from `XYGDataMapping`
     #' @return A new `PKRatioDataMapping` object
-    initialize = function(x = NULL, 
-                          y = NULL, 
+    initialize = function(x = NULL,
+                          y = NULL,
                           ymin = NULL,
                           ymax = NULL,
                           lines = DefaultDataMappingValues$pkRatio,
                           ...) {
       validateIsString(ymin, nullAllowed = TRUE)
       validateIsString(ymax, nullAllowed = TRUE)
-      super$initialize(x=x,y=y,...)
+      super$initialize(x = x, y = y, ...)
       self$lines <- lines
       # If no ymin/ymax defined, map to y to get emtpy errorbars
       self$ymin <- ymin %||% self$y

R/plot-boxwhisker.R

@@ -75,7 +75,6 @@ plotBoxWhisker <- function(data,
 #' @return A `ggplot` object
 #' @keywords internal
 .addBoxWhisker <- function(data, metaData, dataMapping, plotConfiguration, plotObject) {
-
   # Get the box plot quantiles from dataMapping
   mapData <- dataMapping$getBoxWhiskerLimits(data)
   # Convert the mapping into characters usable by aes_string

R/plot-ddiratio.R

@@ -7,7 +7,7 @@
 #' if DDI Ratio plot is drawn as residuals vs observed, instead of predicted vs observed.
 #' @param foldDistance Numeric values of fold distance lines to display in log plots.
 #' This argument is internally translated into `lines` field of `dataMapping`.
-#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. 
+#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive.
 #' In particular, line of identity corresponds to a `foldDistance` of `1`.
 #' @param deltaGuest Numeric value parameter of Guest function
 #' @param dataMapping
@@ -95,7 +95,7 @@ plotDDIRatio <- function(data,
       size = .getAestheticValues(n = 1, selectionKey = plotConfiguration$lines$size, position = lineIndex, aesthetic = "size")
     )
 
-  
+
   eval(.parseAddUncertaintyLayer())
   eval(.parseAddScatterLayer())
   # Define shapes and colors based on plotConfiguration$points properties

R/plot-obs-vs-pred.R

@@ -5,7 +5,7 @@
 #' @inheritParams addScatter
 #' @param foldDistance Numeric values of fold distance lines to display in log plots.
 #' This argument is internally translated into `lines` field of `dataMapping`.
-#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. 
+#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive.
 #' In particular, line of identity corresponds to a `foldDistance` of `1`.
 #' @param smoother Optional name of smoother function:
 #' \itemize{

R/plot-pkratio.R

@@ -5,7 +5,7 @@
 #' @inheritParams addScatter
 #' @param foldDistance Numeric values of fold distance lines to display in log plots.
 #' This argument is internally translated into `lines` field of `dataMapping`.
-#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. 
+#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive.
 #' In particular, line of identity corresponds to a `foldDistance` of `1`.
 #' @param dataMapping
 #' A `PKRatioDataMapping` object mapping `x`, `y` and aesthetic groups to their variable names of `data`.

R/plotconfiguration-legend.R

@@ -27,14 +27,14 @@ LegendConfiguration <- R6::R6Class(
       private$.background <- background %||% currentTheme$background$legend
 
       # Title properties
-      if(!isOfType(title, "Label")){
-      title <- asLabel(
-        text = title %||% currentTheme$background$legendTitle,
-        font = currentTheme$fonts$legendTitle
+      if (!isOfType(title, "Label")) {
+        title <- asLabel(
+          text = title %||% currentTheme$background$legendTitle,
+          font = currentTheme$fonts$legendTitle
         )
       }
       private$.title <- title
-      
+
       private$.caption <- caption %||% data.frame()
     },
 
@@ -54,13 +54,13 @@ LegendConfiguration <- R6::R6Class(
       # Update legend title for all aesthetic properties to prevent unwanted split of legends
       updateLegendTitleExpression <- parse(text = paste0(
         "plotObject <- plotObject + ggplot2::guides(",
-        names(AestheticProperties), " = guide_legend(", 
+        names(AestheticProperties), " = guide_legend(",
         "title = private$.title$text,",
         "title.theme = private$.title$createPlotFont())",
         ")"
       ))
       eval(updateLegendTitleExpression)
-      
+
       # Update legend position and alignment
       legendPosition <- .createPlotLegendPosition(private$.position)
 

R/plotconfiguration.R

@@ -97,7 +97,6 @@ PlotConfiguration <- R6::R6Class(
                           data = NULL,
                           metaData = NULL,
                           dataMapping = NULL) {
-
       # Label configuration
       # validation of the input is done within the creation of the object
       private$.labels <- LabelConfiguration$new(

R/themes.R

@@ -257,7 +257,6 @@ ThemeAestheticMaps <- R6::R6Class(
                           size = NULL,
                           linetype = NULL,
                           alpha = NULL) {
-
       # Validate necessary input
       validateIsString(color, nullAllowed = TRUE)
       validateIsString(fill, nullAllowed = TRUE)
@@ -316,7 +315,6 @@ ThemeAestheticSelections <- R6::R6Class(
                           size = NULL,
                           linetype = NULL,
                           alpha = NULL) {
-
       # Associate to each field its value
       initializeExpression <- parse(text = paste0("self$", names(AestheticProperties), " <- ", names(AestheticProperties), " %||% 'first'"))
       eval(initializeExpression)
@@ -388,7 +386,6 @@ ThemePlotConfigurations <- R6::R6Class(
                           plotBoxWhisker = NULL,
                           plotTornado = NULL,
                           plotHistogram = NULL) {
-
       # Validate necessary input
       atomPlotInputs <- c("addScatter", "addLine", "addRibbon", "addErrorbar")
       moleculePlotInputs <- c("plotPKRatio", "plotDDIRatio", "plotTimeProfile", "plotObsVsPred", "plotBoxWhisker", "plotTornado", "plotHistogram")

R/timeprofile-datamapping.R

@@ -26,7 +26,6 @@ TimeProfileDataMapping <- R6::R6Class(
                           fill = NULL,
                           linetype = NULL,
                           data = NULL) {
-
       # .smartMapping is available in utilities-mapping.R
       smartMap <- .smartMapping(data)
       super$initialize(

R/tlf-env.R

@@ -31,7 +31,7 @@ setDefaultLegendPosition <- function(position) {
 #' @export
 setDefaultLegendTitle <- function(title) {
   validateIsOfType(title, c("character", "Label"), nullAllowed = TRUE)
-  if(isOfType(title, "Label")){
+  if (isOfType(title, "Label")) {
     tlfEnv$currentTheme$fonts$legendTitle <- title$font
     tlfEnv$currentTheme$background$legendTitle <- title$text
     return(invisible())

R/utilities-axis.R

@@ -218,11 +218,11 @@ getPiTickLabels <- function(ticks) {
 
 #' @title .removeInfiniteValues
 #' @description Censor/remove any values outside of range
-#' Caution, removing infinite values can cause issues with ribbons 
+#' Caution, removing infinite values can cause issues with ribbons
 #' which can use such infinite values for filling a range
 #' @param x numeric vector of values to manipulate
 #' @param range numeric vector of length two giving desired output range
 #' @keywords internal
-.removeInfiniteValues <- function(x, range = c(0,1)){
+.removeInfiniteValues <- function(x, range = c(0, 1)) {
   scales::censor(x, range, only.finite = FALSE)
-}
+}

R/utilities-legend.R

@@ -75,13 +75,13 @@ setLegendTitle <- function(plotObject,
                            title = NULL) {
   validateIsOfType(plotObject, "ggplot")
   validateIsOfType(title, c("character", "Label"), nullAllowed = TRUE)
-  
+
   # Clone plotConfiguration into a new plot object
   # Prevents update of R6 class being spread to plotObject
   newPlotObject <- plotObject
   newPlotObject$plotConfiguration <- plotObject$plotConfiguration$clone(deep = TRUE)
   legend <- newPlotObject$plotConfiguration$legend
-  if(isOfType(title, "character")){
+  if (isOfType(title, "character")) {
     title <- asLabel(title, font = legend$title$font)
   }
   legend$title <- title %||% legend$title

R/utilities-mapping.R

@@ -5,13 +5,16 @@
 }
 
 
-.binNumericCol <- function(binLimits, currentDataCol) { # function to iterate through a numeric column and find elements that fall within bin limits.  Returns a logical column of the same size as the input data column.
+.binNumericCol <- function(binLimits, currentDataCol) {
+  # function to iterate through a numeric column and find elements that fall within bin limits.  Returns a logical column of the same size as the input data column.
   .checkIfNotNumeric(currentDataCol, msg = "Dataframe column entries to be binned must be numeric.") # check that dataDf points to be binned are numeric
   sapply(binLimits, .checkIfNotNumeric, msg = "Bin limits must be numeric") # check that all bin limits are numeric
-  if (!(length(binLimits) == 2)) { # check that bin limits are of length 2.
+  if (!(length(binLimits) == 2)) {
+    # check that bin limits are of length 2.
     stop("Each element of bin limits list must be a vector of length 2.")
   }
-  if (!(binLimits[2] > binLimits[1])) { # check that bin limits are in increasing order
+  if (!(binLimits[2] > binLimits[1])) {
+    # check that bin limits are in increasing order
     stop("Bin limits must be increasing.")
   }
   dataPointsInGrp <- sapply(currentDataCol, function(x) {
@@ -25,10 +28,13 @@
 .findColumnEntriesInGroups <- function(dataDf, groupingDfRow) {
   groupingDataColumns <- dataDf[colnames(groupingDfRow)] # get columns from dataDf corresponding to column headings in groupingDf (excluding the last column heading in groupingDf)
   logicMatrix <- matrix(rep(FALSE, nrow(dataDf) * ncol(groupingDfRow)), nrow(dataDf))
-  for (n in seq(1, ncol(groupingDfRow))) { # for each column of the groupingDf
-    if (is.list(groupingDfRow[[n]])) { # case where a list is supplied for binning
+  for (n in seq(1, ncol(groupingDfRow))) {
+    # for each column of the groupingDf
+    if (is.list(groupingDfRow[[n]])) {
+      # case where a list is supplied for binning
       logicMatrix[, n] <- .binNumericCol(groupingDfRow[[n]][[1]], groupingDataColumns[[n]]) # check if each column entry lies within bin limits.  If yes, return TRUE for that entry, else FALSE.
-    } else { # case where there is no binning, only matching between caption dataframe entries and dataDf column entries
+    } else {
+      # case where there is no binning, only matching between caption dataframe entries and dataDf column entries
       logicMatrix[, n] <- sapply(groupingDataColumns[[n]], function(x) {
         return(x == groupingDfRow[[n]])
       }) # check if each column entry matches groupingDf element.  If yes, return TRUE for that entry, else FALSE.
@@ -45,10 +51,13 @@
   stopifnot(ncol(groupingDf) > 1)
   vecIndxGroupingDfRows <- seq(1, nrow(groupingDf)) # vector of factor levels associated with each caption
   groupingFactorColumn <- rep(0, nrow(dataDf)) # vector that is to be populated with factor levels that determine caption
-  for (k in vecIndxGroupingDfRows) { # for each caption
+  for (k in vecIndxGroupingDfRows) {
+    # for each caption
     logicMatrix <- .findColumnEntriesInGroups(dataDf, groupingDf[k, -ncol(groupingDf), drop = FALSE]) # call function to test if each column entry falls within the grouping
-    for (m in seq(1, nrow(dataDf))) { # for each row of dataDf
-      if (all(logicMatrix[m, ])) { # if entire dataDf row matches groupingDf row
+    for (m in seq(1, nrow(dataDf))) {
+      # for each row of dataDf
+      if (all(logicMatrix[m, ])) {
+        # if entire dataDf row matches groupingDf row
         groupingFactorColumn[m] <- vecIndxGroupingDfRows[k] # set factor level in groupingFactorColumn to k
       }
     }
@@ -89,7 +98,6 @@
 #' # Get captions separating variables witha space (character " ")
 #' getDefaultCaptions(data, metaData, sep = " ")
 getDefaultCaptions <- function(data, metaData, variableList = colnames(data), sep = "-") {
-
   # Check that the grouping is in the list of data variables
   stopifnot(variableList %in% colnames(data))
 
@@ -274,7 +282,7 @@ DefaultDataMappingValues <- list(
 #' Get list of values to provide to `lines` argument of `dataMapping` objects.
 #' The `lines` are internally used as argument of `geom_hline` and `geom_abline` from `ggplot2`
 #' @param foldDistance Numeric values
-#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive. 
+#' __Caution__: this argument is meant for log scaled plots and since fold distance is a ratio it is expected positive.
 #' In particular, line of identity corresponds to a `foldDistance` of `1`.
 #' @return A list of numeric values
 #' @export
@@ -317,9 +325,9 @@ getLinesFromFoldDistance <- function(foldDistance) {
 }
 
 .getAggregatedData <- function(data,
-                              xParameterName,
-                              yParameterName,
-                              xParameterBreaks = NULL) {
+                               xParameterName,
+                               yParameterName,
+                               xParameterBreaks = NULL) {
   xParameterBreaks <- xParameterBreaks %||% tlfEnv$defaultAggregation$bins
   xParameterBins <- cut(data[, xParameterName], breaks = xParameterBreaks)
 

inst/theme-maker/app.R

@@ -142,7 +142,6 @@ ui <- fluidPage(
 
 #---------- Server ----------#
 server <- function(input, output) {
-
   #---------- Interactive way of updating aesthetic map element ----------#
   getColorMapValue <- reactive({
     jsonTheme$aestheticMaps$color[input$colorMapIndex]
@@ -296,7 +295,6 @@ server <- function(input, output) {
   })
 
   output$samplePlot <- renderPlot({
-
     # Reactive function that update theme object
     updateTheme()
     plotConfiguration <- PlotConfiguration$new(title = "title", subtitle = "subtitle", xlabel = "xlabel", ylabel = "ylabel", caption = "caption")